Major and Commander
by B0rnlucky
Summary: Shepard gave everything she had to protect Humanity. She figured her fight was over and that she'd be able to finally sit down and have that drink with her boyfriend. Instead she finds herself face to face with a new threat in a new galaxy, and he only piece of sanity she has left is lost. If she ever hopes to find Garrus, she'll have to do what she does best: Save the Galaxy.
1. Chapter 1

**Major and Commander**

 **Chapter 1: Once More Unto the Breach**

* * *

"That's not a whole lot of good options, Shepard." Garrus said.

"I know Garrus." Shepard coughed. Her whole body felt like she had gone twelve rounds with a Krogan then been hit by a Vorcha flame thrower.

Garrus looked over at his mate as she struggled to stay standing. His heart had stopped when he saw her get hit by Harbinger's beam weapon. Only to have it start beating again when he picked her up and she cried out in pain. He had dragged her to the beam and up to the Citadel. After finally dealing with the Illusive Man they were now trying to find a way to fire the Crucible. Which had led them to here.

Three impossible choices.

Shepard was silent but her mind was racing. She didn't have a whole lot of options, and she didn't have a whole lot of time. While she waited Admiral Hackett and the fleets were being wiped out. She knew there was really only one choice she could make. She wouldn't doom the Geth after having come so far and she certainly wouldn't try and control the Reapers, for fear that she would become just another tyrant. That left only one choice.

"What do you say Garrus? One more ride?" She asked.

Garrus stared at her with those deep cobalt blue eyes, "I thought you'd never ask Shepard."

Together they stumbled their way to the energy matrix. Before they took the plunge Shepard stopped. She mustered her strength and pulled Garrus' head down. "I couldn't have done this without you Garrus."

"Sure you could have, maybe not as flashy but. . ." Garrus smiled. "Shepard I-" Shepard reached up and kissed him.

"I know Garrus." She said softly. "Come on, we got a bar to get to."

Garrus, smiled. He wrapped his arms around her and together they fell into the energy matrix.

* * *

"Rodney what's going on?" Weir shouted.

"We've got an incoming wormhole!" The Canadian shouted.

"Close the shield!"

"I've already tried, there's some kind of energy surge coming through the gate it's locked us out of the controls!"

Elizabeth looked over at Major Sheppard and nodded.

"I need security teams one and two to the gate room now!" Sheppard called out over the comms.

Elizabeth and the rest of the gate room personal watched as the gate dialed up and the wormhole established.

"If this is a Wraith attack we aren't ready." Rodney said.

"I know McKay. We'll just have to handle the situation."

Everyone in the gate room watched as a series of pulses ran through the gate. A low hum accompanied each energy pulse. The energy continued to build and soon bolts of electricity jumped from the gate. One struck the wall right in front of Sheppard and he flinched at the brilliant light and sound.

"It's getting too hot here, everyone fall back!" John yelled. Suddenly the gate began to roar and all the sudden someone came flying through.

They slammed into to stairs that lead up to the stargate command center. He winced at the crunching sound the person made when they hit the stairs. With a flash the stargate shut down. Sheppard sprinted out from cover and ran over to whoever had come out of the gate.

He stopped when he got a good look at her. In a word she looked like hell. She was wearing some form of body armor, it might have been functional at some point but now it looked like pieces of blackened charcoal. What little part of her skin he could see was burnt and blistered and she was having trouble breathing. Despite all the bruises he could tell the woman was a looker.

"I need a medical team to the gate room now!" John yelled.

* * *

"Alright Dr. Becket, what have you got on our latest guest."

"In a word Commander, she's bloody weird."

Dr. Weir raised her eyebrow at her doctor. "What do you mean?"

"When we brought her in she was in bad shape, but she's healing at an accelerated rate. I took a blood sample and well . . ." He trailed off.

"What is it doctor?"

"It's like her body's in the middle of a complete genetic re-write. Her cells show both organic and synthetic properties and it's spreading. It's unlike anything I've ever seen before."

"Is she contagious?" Dr. Weir asked in alarm.

"I don't believe so, but I've placed her in isolation just to be sure, but that's not even half of what I found. I did a full body scan these are the results." Dr. Becket handed over a folder full of images. "Even before what ever happened to her, this woman had a number of cybernetic implants like nothing I've ever seen. I estimate fifty percent of her body's functions were regulated by these implants, but she shows no signs of rejection."

"That's incredible." Dr. Weir said. While her degree had nothing to do with medicine even she could see how advanced these implants were. Whoever this woman was their medical technology was far superior to anything she had ever seen.

"I'm more interested in the weapons she had on her." John said.

Dr. Weir, nodded and looked at Rodney, "McKay, what have you learned."

"Honestly not much." Rodney admitted. "I managed to get her pistol unfolded and Major Shepard test fired a few rounds from it."

"The thing packs a punch." John added.

"Yes, anything that fires a round at a good percentage of light speed would indeed pack a punch." Rodney deadpanned.

"Wait," Dr. Weir interrupted in shock, "what exactly constitutes a sizable percent of light speed."

"1.12%" Rodney rattled off.

Dr. Weir's eye's widened, "That's impressive. How is that possible?"

"As far as I can tell there is some sort of unidentified element at generates a Dark Energy field. I think that might be the power source for the weapon. I don't want to go opening it up until I know more." Rodney admitted.

"That's not like you Rodney. Normally I have to try and convince you to not go poking around alien technology we don't understand yet, what's changed?" Dr. Weir asked.

"The last time I tried out a new technology without understanding it I nearly starved to death. Besides Dark Energy isn't nearly as understood as I'd like it to be. As far as we can tell this is the same energy field that helps hold the universe together, but somehow her people have managed to turn it into a weapon."

 _"Dr. Becket, your patient is waking up."_ Someone called over the radio.

"Bloody hell, I didn't think she'd wake up that fast."

Weir looked over at her chief medical officer in concern, "Dismissed everyone, let's go meet our guest Dr. Becket."

* * *

Shepard slowly became aware of her surroundings. At first all she could feel were the agonizing protests in her body as she subtly shifted her weight in an effort to get comfortable. Soon enough she realized that wasn't going to work and she slowly opened her eyes. She gasped as brilliant white light pierced her eyes forcing her to shut her eyelids again.

She jerked when she felt a hand press on her shoulder.

"Please don't try to move ma'am. Dr. Becket's on his way." A voice said calmly.

"Where am I?" Shepard tried to demand, but her voice came out more like a harsh croak.

"You're safe. Please be patient Dr. Becket is on his way." The voice said soothingly.

Shepard tried opening her eye's again but she could only make out a vaguely human shape before the light became too much for her and she closed them again.

Suddenly she heard another group of voices another group of voices. She could only assume that whoever Dr. Becket was must have arrived.

"Ma'am can you hear me?" a light brogue accented voice asked her.

"I can hear fine, but there's something wrong with my eyes. Everything's too bright." Shepard answered.

She heard rustling and Dr. Becket say, "Turn down the lights as far as you can please she might be photosensitive right now." Shepard assumed he was talking to his nurse.

"Ma'am I'd like you to try opening your eye's now." She heard Dr. Becket say.

Shepard did so slowly and took in her surroundings. It was obviously much darker than before but she still had to squint in order to see much of anything. She was lying on her back in what had to be the strangest medical ward she had ever seen. Instead of sterile white walls like she was used to, the walls here were made of stone, granite or something similar, and were lightly embossed with strange hieroglyphics.

The man standing before her wore a white lab coat similar to what a doctor would wear in the early 21st century. To his right stood a woman she was wearing some kind of formal uniform that she didn't recognize. There was another man with a round face that was in similar attire, but what caught her attention was the third man. He was wearing a set of BDU's and while he only had a side arm his easy posture was one that she recognized. Shepard had no doubt that if the man wanted he could have his side arm up and pointed at her in less than a second.

"Where am I?" Shepard asked slowly.

"You're in my medical facility here on Atlantis." The man in the lab coat said. "I'm Dr. Becket, this is Dr. Weir."

"Hello." The woman said.

"Dr. McKay." The round faced man waved.

"And Major Sheppard." The military man nodded at her.

Kaya Shepard stared at all of them for a moment before she opened her mouth, "My name is Commander Shepard, Earth Systems Alliance. Where the hell is Atlantis?"

* * *

 **A/N: I just wanted to write this down and see where this goes. Haven been able to write a hole lot lately so here it is.**


	2. Chapter 2

**Major and Commander**

 **Chapter 2: Hope and Disappointment**

* * *

Elizabeth Weir sank into her chair with a groan. Now more than ever she wished she could have a stiff drink in her hand, unfortunately they couldn't afford to waste any space on something so frivolous in their supplies from Earth. Instead she decided to make do with some Athosian wine she'd received as a gift.

"Got any in there for me?" Weir looked up to see John Sheppard standing in the door to her quarters. "Sorry I should have knocked or something." He said looking around at the door frame.

"It's fine John." Weir said giving him a small smile. "I didn't want to drink alone anyway." She grabbed a spare glass and sat down on her couch and poured them both a sizable amount. Before John said anything she gulped down half her glass and refilled it.

"You okay, Elizabeth?" John asked with a raised eyebrow.

Dr. Weir took a deep breath and leaned back with the glass in her hand. "Honestly, I'm not sure." She said.

"I know what you mean." John said.

After Commander Shepard had introduced herself everyone in the room had practically gone into shock. It had taken hours of explanations and technical talk between herself, Dr. McKay, and the Commander to piece together what had happened to Commander Kaya Shepard. Between the three of them they had been able to find the only possible explanation.

The Commander and her boyfriend/mate had been at the heart of a massive Dark Energy discharge. Coupled with the effects of the enormous amounts of Element Zero, of which Weir only had a vague understanding of, Commander Shepard had been shot into a tear in the fabric of space time at many, many times the speed of light. The tunnel of massless ness that she had traveled through had been mistaken as an incoming wormhole by the stargate here in Atlantis. Dr. McKay theorized the only reason she appeared here in Pegasus rather than back in the Milky Way was that by the time the massless corridor had stabilized she had already moved beyond the galactic circle. Her trajectory must have put her close enough for the Atlantis gate to redirect and open a wormhole for her to rematerialize through. As for the time travel, well the laws of physics are pretty much considered general guidelines when one considered the forces at work.

What bothered Dr. Weir the most however wasn't the fact the woman had traveled all the way here from a future Earth that was in a universe so completely different from their own, but what had caused her to take such drastic measures in the first place. The images of the Reapers and their proto-forms would haunt Dr. Weir's nightmares for a while.

"What do you think of her?" John asked suddenly breaking her train of though.

"I think she's been through hell and back." Weir said honestly. The only evidence they had that the Commander was telling the truth was her word and the images that she'd stored on her omni-tool, but it was hard to fake the look in the woman's eye's as she told Weir and her team her story in her fight against the Reapers. Shepard had seen more combat in the last five years than even General Jack O'Neil had in his entire lifetime and against monsters far worse than anything Weir had heard of aside from the Wraith.

"It's a lot to take in." John agreed. He'd seen his fair share of hurt soldiers before, but the Commander was something else entirely. She'd literally carried the weight of the galaxy on her back and had somehow managed to come out on top, but not without scars. "So what are we going to do?" he asked.

"Whatever we can John. If I could sent her home I would but we don't have that ability, the best we can do is make her comfortable and hope for the best. Dealing with displaced universe hopping time travelers fresh from the war of the century wasn't something I was prepared for to be honest." Elizabeth said.

John finished the rest of his wine and stood up. "You'll figure it out Elizabeth. If anyone can help her it's you." He left leaving Elizabeth with her thoughts and a glass of half empty wine.

* * *

As Dr. Weir and Major Sheppard tried to figure out what to do. Kaya walked through the hallways of Atlantis like a woman on a mission. The scuttlebutt must have made the rounds because most of the base personnel gave her a lot of odd looks. Although that might have has something to do with the fact that she was only wearing a hospital gown and that almost fifty percent of her body was covered in rapidly healing scar tissue.

It had taken her the better part of an hour to give the good Dr. Becket the slip, but there was someone she had to find. She had questions she needed to ask and so far there was only one person that seemed to be smart enough to be able to answer them. She ignored the pain in her body as she marched down the corridor.

It took a bit but she finally found the person she was looking for, and conveniently he was in the mess hall. "Dr. McKay." She called out when she reached him.

"Can't a guy go five minutes and eat-" His back had been turned to her and his head had been buried in a data pad so he hadn't seen her walk up, Dr. McKay had stopped his rant midsentence when he realized who had been calling for him.

"Commander Shepard! Should you be up yet?" He practically squeaked.

"Probably not." Shepard agreed. "But I need to talk to you. Will you wait here while I get some food?" She asked.

"Uh sure." McKay said.

Shepard made her way over to the chow line and proceeded to pile her plate full of everything that was available. When she had returned and sat at the table McKay was at he was staring at her with his mouth open.

"What?" She asked.

McKay startled and shook his head, "Sorry, it's just that I don't think I ever seen someone eat that much before."

Shepard would have laughed if she didn't have a mouth full of food. "It's alright, the same implants that were used to help bring me back to life do wonders for my body. The make me stronger, faster, and heal quicker that a normal human, but they trade off is my body burns a lot more calories than normal. When I get injured they speed up my metabolic processes even more to help aid with the healing. I'm starving."

McKay was decent enough to go back to whatever he was working on before she had interrupted him while she ate. He was a little nervous being around the Commander especially considering what she was wearing. She didn't seem to care though so he put it out of his mind. When she was done he looked at her.

"McKay I need to know something. First is it possible for you to recreate the event that brought me here? Is it possible for me to return home?" She asked. There was no sign of pleading in her voice and her eyes were steady and clam. McKay was again reminded what this woman had gone through. It was easy to believe that she'd basically been an intergalactic super spy for all the emotion she was showing at the moment.

"Technically it's possible. We've had a few instances where we've dealt with alternate universes in the past and we've even dealt with time travel before," He saw the faintest glimmer of hope in her eyes, "but never from somewhere so different than out own." He finished. "Stargate Command back on Earth has access to a few technologies that allow travel between alternate universes, but they're very unpredictable. I wouldn't even know where to start." He said truthfully.

Shepard nodded. "So possible but realistically beyond the realm of possibility." She said completely unphased. "Next question, There was someone else that was with me when I fell into the energy matrix of the Crucible. If I ended up here is there a possibility that he could be somewhere else in this Galaxy." If Shepard were to be honest with herself getting home was a second priority compared to finding out what had happened to Garrus. So far she'd kept all of those emotions bottled up until she had a chance to get some answers. She'd deal with those once she'd assessed her situation and learned if there was anything to be done.

McKay nodded, "You mean your boyfriend, Garret or something right."

"Garrus, and he's my mate, my. . . husband in human terms." She said slowly. It was the first time McKay had seen her crack even if it was only for a moment.

"That's much more possible." He said softly. The Commander looked up and only now could he see how much she had been hurting. It must have been incredibly painful for to not know what had happened to her friend. "The problem is that his trajectory must have been slightly different from yours there are millions of stargates in this galaxy and we've only just started exploring it. He could be anywhere."

"If he made it to this galaxy then I'll find him. Garrus is one of the best danm soldiers I've known. If he made it than he'll survive. I'll find him."

"That could take years though." McKay argued.

"It doesn't matter. I don't leave my people behind. After what happened on Virmire I swore to myself I'd never do that again or die trying." She said.

It took McKay a few seconds to remember what the Commander was talking about. Shepard had been forced to leave one of her crew behind in a nuclear blast that she had used to destroy a cloning facility early on in her fight against the Reapers.

"Okay, okay. I see I can't persuade you, how can I help?" McKay asked.

Shepard had not been expecting McKay's offer of help, she raised an eyebrow at him. "Well you could teach me how to use that stargate thing so I can start looking as soon as I get better." She said.

"Or you could come with us as we go exploring the galaxy ourselves." A voice said behind her.

Kaya turned around to see John Sheppard standing behind her with his own tray of food. "You'd let me come with you?" She asked.

"I don't see why not. You're probably the most qualified combatant in this entire city and you do have experience fighting galaxy spanning threats." John said.

Commander Shepard narrowed her eyes at what John had said or specifically what he hadn't said. "Something tells me you have your own version of Reapers here. What aren't you telling me?" He voice had become brittle as ice.

John sat down. "Dr. Weir told me not to tell you this just yet but something tells me that if I don't you'll just run off on your own and get yourself into trouble."

"Wouldn't be the first time." Kaya admitted.

"Although I am tempted to just let you go. Who known in a few years maybe you'll have solved all our problems by yourself." John teased.

Kaya wasn't amused and leveled a glare at the Major.

He sighed. "Okay here's what we know so far."

* * *

 **A/N: Hope you guys like the update. Please Read and review**


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